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Job request: 533

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-thrombosis
ID:
qrxmipx2z5cqhdbl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Walker requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 20000

actions:
  generate_covid_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
    outputs:
      highly_sensitive:
        cohort: output/input_covid.csv

  generate_covid_community_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
    outputs:
      highly_sensitive:
        cohort: output/input_covid_community.csv

  generate_pneumonia_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
    outputs:
      highly_sensitive:
        cohort: output/input_pneumonia.csv

  generate_measure_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2020-10-01 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measures*.csv

  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_measures
    needs: [generate_measure_cohort]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_rate.csv

  draw_timeseries:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        graph: output/event_count_time_series.svg

  covid_rates_cohort:
   run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
   needs: [generate_covid_cohort]
   outputs:
     highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta

  covid_community_rates_cohort:
   run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
   needs: [generate_covid_community_cohort]
   outputs:
     highly_sensitive:
        analysis_dataset: output/cohort_rates_covid_community.dta

  pneumonia_rates_cohort:
   run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
   needs: [generate_pneumonia_cohort]
   outputs:
     highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta

  covid_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [covid_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid.csv

  covid_comm_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
    needs: [covid_community_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_community.csv

  pneumonia_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_pneumonia.csv

  baseline_characteristics:
    run: stata-mp:latest analysis/400_baseline_characteristics.do
    needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        tables: output/tabfig/an_descriptiveTable_*.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-thrombosis
Requested by
Alex Walker
Branch
master
Force run dependencies
No
Git commit hash
ef0eaca
Requested actions
  • generate_covid_cohort
  • generate_covid_community_cohort
  • generate_pneumonia_cohort
  • covid_rates_cohort
  • covid_community_rates_cohort
  • pneumonia_rates_cohort
  • covid_rates
  • covid_comm_rates
  • pneumonia_rates
  • baseline_characteristics

Code comparison

Compare the code used in this job request